rs3814526

Variant names:

• chr9-128148408-A-G
• rs3814526

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0761 in 152,254 control chromosomes in the GnomAD database, including 858 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.076 (858 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11594 AN: 152136 Hom.: 861 Cov.: 31

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0689

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0761 AC: 11584 AN: 152254 Hom.: 858 Cov.: 31 AF XY: 0.0799 AC XY: 5947 AN XY: 74438

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0840

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0503 Hom.: 755

Bravo AF: 0.0766

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3814526; hg19: chr9-130910687;